Details


Species	Human
Species subgroup
Subgroup type
Sequence Name	IGLV10-54*04
IUIS Name	IGLV10-54*04
Alternative names	IGLV10-54*i01
Affirmation Level	1
Full Sequence
Coding Sequence
Functionality	ORF
Inference Type	Genomic and rearranged
Mapped	False
Paralogs
Paralog Rep	False

Observations in VDJbase

Inferred sequences in VDJbase that match this sequence:

VDJbase Allele Name	Subjects	Sequence Match
IGLV10-54*01_a228c	24

Un-rearranged Observations

Un-rearranged sequence observations that support this sequence:

Accession	Type	Repository	Start	End
MK308862	Inferred	GenBank	1	294

CDR delineation


CDR1 Start	392
CDR1 End	415
CDR2 Start	467
CDR2 End	475
CDR3 Start	584

Non-Core Regions


UTR 5' Start
UTR 5' End
L-PART1 Start
L-PART1 End
L_PART1
L-PART2 Start	306
L-PART2 End	316
L_PART2	TGTCAGTGGTC
v_rs_start	613
v_rs_end	651
V_HEPTAMER	CACAGTG
V_NONAMER	ATAAAAACT

Extension


3' Extension	CA
3' start
3' end
5' start
5' end

Additional Information


Sequence ID	A00055
Curator	William Lees
Curator address	Birkbeck College, University of London, Malet Street, London
Version	2
Release Date	2023-07-10
Release Notes	Bulk upload of sequences for the AIRR-C Human IG germline sets
Locus	IGL
Sequence Type	V
Gene Subgroup	10
Gene Designation	54
Allele Designation	04

Acknowledgements

Individuals acknowledged as contributing to this sequence:

No Items

Notes

Notes are added by IARC reviewers.


The sequence was first affirmed at IARC Meeting 53 on April 14th 2020, where it was noted: “The sequence was seen in 1.79% of all unmutated rearrangements, with 11279 sequences including 2138 perfect matches to the inferred allele. There was abundant variation in the CDR3 regions of the aligned sequences. The IGLV10-54*01 allele was also present in the genotype, at a similar frequency (1.77% of all unmutated sequences; 7826 sequences; 2117 unmutated sequences). Haplotype data is unavailable. Plots of the final 3’ nucleotides showed a high level of variability, making it impossible to determine the final three nucleotides with certainty. The sequence, up to and including nucleotide 339, was affirmed as a Level 1 sequence. Uncertainty regarding nucleotides 340-341 will be indicated in IARC and OGRDB publications by two dots at the end of the affirmed sequence.” Additional information for this sequence was imported into OGRDB via bulk update with the following notes: Sequence annotation is based on Genbank sample MW316678

The sequence was first affirmed at IARC Meeting 53 on April 14th 2020, where it was noted:

“The sequence was seen in 1.79% of all unmutated rearrangements, with 11279 sequences including 2138 perfect matches to the inferred allele. There was abundant variation in the CDR3 regions of the aligned sequences. The IGLV10-54*01 allele was also present in the genotype, at a similar frequency (1.77% of all unmutated sequences; 7826 sequences; 2117 unmutated sequences). Haplotype data is unavailable. Plots of the final 3’ nucleotides showed a high level of variability, making it impossible to determine the final three nucleotides with certainty. The sequence, up to and including nucleotide 339, was affirmed as a Level 1 sequence. Uncertainty regarding nucleotides 340-341 will be indicated in IARC and OGRDB publications by two dots at the end of the affirmed sequence.”

Additional information for this sequence was imported into OGRDB via bulk update with the following notes:
Sequence annotation is based on Genbank sample MW316678

Attachments

No Items

History

History logs the times and reasons for the publication of each version of this sequence.


Andrew Collins 2020-07-30 12:58:46	Version 1 published Submission published by IARC on July 30th 2020.


Mats Ohlin 2021-04-29 22:33:15	*IMGT Name updated to IGLV10-5404** IMGT Name updated.


William Lees 2023-07-10 11:24:46	Version 2 published Bulk upload of sequences for the AIRR-C Human IG germline sets

Changes from previous version

	v1	v2
Curator		William Lees
Curator address	School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney Australia	Birkbeck College, University of London, Malet Street, London
Sequence Name	IGLV10-54*i01	IGLV10-54*04
Alternative names		IGLV10-54*i01
Mapped		False
Functionality	F	ORF
Inference Type	Rearranged Only	Genomic and rearranged
Species subgroup
Subgroup type
Allele Designation	i01	04
Full Sequence
Gene start	1	317
Gene end	294	610
L-PART2 Start		306
L-PART2 End		316
CDR1 Start	76	392
CDR1 End	99	415
CDR2 Start	151	467
CDR2 End	159	475
CDR3 Start	268	584
v_rs_start		613
v_rs_end		651
Paralog Rep		False
Extension?	False	True
3' Extension		CA
5' Extension
curational_tags		likely_full-length
Notes		changed

Versions

All published versions of this sequence.

Sequence Name	IMGT Name	Alternative names	Inference Type	Affirmation Level	Subgroup type	Gene start	Gene end	L-PART1 Start	L-PART1 End	L-PART2 Start	L-PART2 End	CDR1 Start	CDR1 End	CDR2 Start	CDR2 End	CDR3 Start	v_rs_start	v_rs_end	Codon Frame	Version	Date
IGLV10-54*i01	IGLV10-54*04		Rearranged Only	1		1	294					76	99	151	159	268				1	2020-07-30
IGLV10-54*04	IGLV10-54*04	IGLV10-54*i01	Genomic and rearranged	1		317	610			306	316	392	415	467	475	584	613	651		2	2023-07-10
IGLV10-54*04	IGLV10-54*04	IGLV10-54*i01	Genomic and rearranged	1	none	170	463	1	46	159	169	245	268	320	328	437	466	504	1	3	2024-02-22